From: jc guo (guojc123_at_gmail.com)
Date: Fri Oct 16 2015 - 00:11:18 CDT
Hi,
I saw some were asking about this,
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/3508.html
but I did not get clear answer from above, is the replica exchange not work
for single node? only works on the cluster? since I do not know how to find
my nodelist in our workstation, so could you help me.
I download source code of NAMD 2.10, and follow the compile step in
note.txt, such as,
tar xzf NAMD_2.10_Source.tar.gz
cd NAMD_2.10_Source
tar xf charm-6.6.1.tar
Build and test the Charm++/Converse library (MPI version):
cd charm-6.6.1
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
cd mpi-linux-x86_64/tests/charm++/megatest
make pgm
mpirun -n 4 ./pgm (run as any other MPI program on your cluster)
cd ../../../../..
Download and install TCL and FFTW libraries:
(cd to NAMD_2.10_Source if you're not already there)
wget
http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
tar xzf fftw-linux-x86_64.tar.gz
mv linux-x86_64 fftw
wget
http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
wget
http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
tar xzf tcl8.5.9-linux-x86_64.tar.gz
tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
mv tcl8.5.9-linux-x86_64 tcl
mv tcl8.5.9-linux-x86_64-threaded tcl-threaded
Optionally edit various configuration files:
(not needed if charm-6.6.1, fftw, and tcl are in NAMD_2.10_Source)
already in same directory.
Set up build directory and compile:
MPI version: ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64
cd Linux-x86_64-g++
make (or gmake -j4, which should run faster)
Quick tests using one and two processes (network version):
(this is a 66-atom simulation so don't expect any speedup)
./namd2
./namd2 src/alanin
./charmrun +p2 ./namd2
./charmrun +p2 ./namd2 src/alanin
Longer test using four processes:
wget http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz
tar xzf apoa1.tar.gz
./charmrun +p4 ./namd2 apoa1/apoa1.namd
above two test case works, but when I ran replica module in NAMD, follows
such steps,
cd example (in replica directory)
mkdir output
(cd output; mkdir 0 1 2 3 4 5 6 7)
mpirun namd2 +replicas 8 job0.conf +stdout output/%d/job0.%d.log
error happens, likes,
Converse/Charm++ Commit ID:
v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
Warning> Randomization of stack pointer is turned on in kernel, thread
migration may not work! Run 'echo 0 >
/proc/sys/kernel/randomize_va_space' as root to disable it, or try run
with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> cpu topology info is gathered in 0.001 seconds.
Info: NAMD 2.10 for Linux-x86_64-MPI
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60601 for mpi-linux-x86_64
Info: Built Mon Sep 28 02:01:43 SGT 2015 by tanmingchen on tanmingchen
Info: 1 NAMD 2.10 Linux-x86_64-MPI 1 tanmingchen tanmingchen
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0263531 s
Info: 83.3789 MB of memory in use based on /proc/self/stat
Info: Configuration file is ../lib/replica/example/job0.conf
Info: Changed directory to ../lib/replica/example
replica_neighbors proc passes internal consistency check
TCL: Reduction callback proc set to save_callback
TCL: can't read "temperature": no such variable
FATAL ERROR: can't read "temperature": no such variable
while executing
"temperature $temperature"
invoked from within
"if {$i_run} { #restart
bincoordinates $restart_root.$replica_id.coor
binvelocities $restart_root.$replica_id.vel
extendedSystem $restart_root.$r..."
(file "~/gg/namd/NAMD_2.10_Source/lib/replica/umbrella.namd" line 90)
invoked from within
"source ~/gg/namd/NAMD_2.10_Source/lib/replica/umbrella.namd"
invoked from within
"if { ! [catch numPes] } { source
~/gg/namd/NAMD_2.10_Source/lib/replica/umbrella.namd}"
(file "job0.conf" line 5)
[0] Stack Traceback:
[0:0] CmiAbortHelper+0x63 [0xc56ca3]
[0:1] _Z8NAMD_diePKc+0x84 [0x5e5a94]
[0:2] _Z18after_backend_initiPPc+0x212 [0x5ea7d2]
[0:3] main+0x1a [0x57f34a]
[0:4] __libc_start_main+0xf5 [0x7f7e901dfec5]
[0:5] [0x58217c]
could you help me? Is replica only can work on cluster, not support my
workstation's information looks like?
grep 'core id' /proc/cpuinfo | sort -u | wc -l
4
grep 'processor' /proc/cpuinfo | sort -u | wc -l
8
Sorry to disturb you, hope I could get some help from any of you.
Best regards,
JC Guo
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